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Yorodumi- PDB-2e9c: E. coli undecaprenyl pyrophosphate synthase in complex with BPH-675 -
+Open data
-Basic information
Entry | Database: PDB / ID: 2e9c | ||||||
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Title | E. coli undecaprenyl pyrophosphate synthase in complex with BPH-675 | ||||||
Components | Undecaprenyl pyrophosphate synthetase | ||||||
Keywords | TRANSFERASE / cell wall / prenyltransferase / farnesyl pyrophosphate / bisphosphonate / antibiotic | ||||||
Function / homology | Function and homology information Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / manganese ion binding ...Gram-negative-bacterium-type cell wall biogenesis / ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] / di-trans,poly-cis-undecaprenyl-diphosphate synthase activity / Z-farnesyl diphosphate synthase activity / polyprenol biosynthetic process / polyprenyltransferase activity / small molecule binding / peptidoglycan biosynthetic process / cell wall organization / manganese ion binding / regulation of cell shape / cell cycle / cell division / magnesium ion binding / protein homodimerization activity / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Guo, R.T. / Ko, T.P. / Cao, R. / Liang, P.H. / Oldfield, E. / Wang, A.H.J. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Bisphosphonates target multiple sites in both cis- and trans-prenyltransferases Authors: Guo, R.T. / Cao, R. / Liang, P.H. / Ko, T.P. / Chang, T.H. / Hudock, M.P. / Jeng, W.Y. / Chen, C.K.M. / Zhang, Y. / Song, Y. / Kuo, C.J. / Yin, F. / Oldfield, E. / Wang, A.H.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e9c.cif.gz | 105.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e9c.ent.gz | 81.2 KB | Display | PDB format |
PDBx/mmJSON format | 2e9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2e9c_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 2e9c_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2e9c_validation.xml.gz | 24.7 KB | Display | |
Data in CIF | 2e9c_validation.cif.gz | 33.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/2e9c ftp://data.pdbj.org/pub/pdb/validation_reports/e9/2e9c | HTTPS FTP |
-Related structure data
Related structure data | 2e8tC 2e8uC 2e8vC 2e8wC 2e8xC 2e90C 2e91C 2e92C 2e93C 2e94C 2e95C 2e98C 2e99C 2e9aC 2e9dC 1jp3S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 28481.127 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pET32/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) References: UniProt: P60472, ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] #2: Chemical | ChemComp-B75 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.63 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20% Ethylene glycol, 2-5% PEG35K, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Details: mirrors |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. all: 30912 / Num. obs: 30788 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Redundancy: 7.23 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 39.9 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.446 / Mean I/σ(I) obs: 4.6 / Num. unique all: 3048 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1JP3 Resolution: 2.05→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 46.41 Å2 | |||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.25 Å / Luzzati sigma a obs: 0.2 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.12 Å
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